Pharmacogenetics

Question 1

What is pharmacogenomics?

Answer 1

A subdiscipline of pharmacogenetics that uses tools to survey the entire genome to assess the genetic determinants of drug response

Question 2

What is a polymorphism?

Answer 2

A variation in DNA sequence that present at a frequency of at least 1% in a population

Question 3

What is the difference between a genotyping and phenotyping test for metabolic enzymes?

Answer 3

Genotyping - test DNA for presence of specific polymorphism
Phenotyping - administer a probe substrate known to be metabolized by the substrate of question, and monitor blood levels to assay metabolism

Question 4

What are some of the positive clinical applications of pharmacogenetics?

Answer 4

1. Better screening for potential drug candidates
2. Better identification of therapeutic dose
3. Improved ability to select potential protein targets for drug development
4. Better ability to ID patients who might e at increased risk for therapeutic failure / adverse drug reaction

Question 5

What is a “phenotype-to-genotype” approach?

Answer 5

A method of identifying pharmacogenetic traits by looking at drug response outliers and comparing them to normal to determine the genetic basis for the response

Question 6

What is the debrisoquine polymorphism example?

Answer 6

Dr. Robert Smith was developing an anti-hypertensive drug. Took a dose of it, and had orthostatic hypertension for several days. Was found to have a CYP2D6 mutation which made him metabolically deficient in drug processing -> drug product found in his urine even days later.

Question 7

What can cause an extensive metabolizer of debrisoquine vs poor vs ultrarapid?

Answer 7

Poor = mutant CYP2D6 alleles
Extensive = normal
Ultrarapid = multiple copies of CYP2D6

Question 8

What is the newest approach for discovering pharmacogenetic traits?

Answer 8

Reverse genetic, genotype-to-phenotype approach

Use GWAS (Genome wide association studies) to identify genetic polymorphisms, and then determine if these associate with a phenotypic variability.

Question 9

What have twin studies shown regarding drug metabolism?

Answer 9

Drug metabolism is highly heritable -> monozygotic twins are much more similar than dizygotic

Question 10

What is a multigenerational kindred study?

Answer 10

One that studies interfamily vs intrafamily variability in drug metabolism

Question 11

What is meant by autosomal dominant, recessive, and co-dominant genetic inheritance of drug metabolism and which is most common?

Answer 11

Dominant - need just one copy of the mutant allele to have impaired metabolism
Recessive - need both copies of mutant allele to have impaired metabolism
Co-dominant - most common - drug metabolism is based on copy number. Those heterozygous for the mutant allele will have a slightly slower metabolism than those with two functional alleles

Question 12

When is it easy vs hard to make accurate predictions about drug metabolism based on genetics?

Answer 12

Monogenic traits - easy, based on one gene
Multigenic - based on multiple genes, can be near impossible to predict phenotype because of all the different combinations

Question 13

What type of system governs warfarin metabolism?

Answer 13

Digenic trait -> two genes. One is fully dominant, the other is co-dominant.

Question 14

What are the three major types of genetic polymorphisms and which is most common?

Answer 14

1. SNPs - single nucleotide repeats, most common, every 100 to 1000 bp
2. Insertions and deletions
3. Copy number variants

Question 15

What is a non-synonymous vs synonymous SNP?

Answer 15

Two types of SNPs occuring in the coding region (cSNPs)

Non-synonymous = missense - change in amino acid

Synonymous = sense - silent - can still lead to a meaningful change in protein due to changes in processing of protein speed -> change in folding / conformation

Question 16

What is a nonsense SNP?

Answer 16

Base pair change introduces a stop codon

Question 17

How can polymorphisms in non-coding regions be relevant?

Answer 17

In 5’ or 3’ UTRs can alter cis-elements which determine mRNA translation or stability.

Can alter promoter or ehancer

Can lead to alternate splice sites if near exon-intron boundaries (introducing frameshift or premature stop)

can affect intergenic regions

Question 18

How can a SNP in an intergenic region be impactful?

Answer 18

May affect DNA tertiary structure and interaction with chromatin, topoisomerases, or DNA replication

Question 19

What two sites for SNPs show the largest association with human variants in disease?

Answer 19

1. Intronic - due to splice site changes

2. Intergenic - due to reasons described previously

Question 20

What is a haplotype? How does this relate to SNP function?

Answer 20

A specific set of SNPs on a single chromosome or gene

(if two bases are known to vary in the gene, the haplotype you have would just be the two bases associated with those numbers)

Some SNPs are only relevant when in combination with other SNPs, others are only relevant when alone

Question 21

What is linkage disequilibrium?

Answer 21

When the genotypes at two loci are not independent of one another -> one gene tends to be inherited with another

Question 22

What is complete linkage disequilibrium?

Answer 22

Genotypes at two loci always occur together

i.e. when one SNP is present, a second SNP is always present.

Question 23

What factors of a drug can make a pharmacogenetic polymorphism more important?

Answer 23

1. Narrowness of therapeutic index / sharpness of dose response curve
2. Limited availability of alternative clearance pathways / enzymes
3. Absence of alternative drugs

Question 24

Why might a drug polymorphism be maintained in a population?

Answer 24

Without selective pressure such as metabolism of a drug to cure a disease, there may be no issue with a variation in drug response.

Question 25

What is the acetylation polymorphism and what is the major gene affected?

Answer 25

NAT2 is primarily affected

“Fast” acetylation is dominant, individual must have two “slow” alleles to see an affect. Large ethnic variability, with altered response to many chemicals including caffein and 4-aminobiphenyl (bladder carcinogen)

Question 26

Why is acetylation polymorphism clinically important?

Answer 26

Slow acetylators are more prone to hemolytic anemia during treatment with sulfra drugs, and have a higher incidence of bladder cancer

Question 27

Why do white people tend to get way less flushed than Asians when drinking alcohol?

Answer 27

Asians often have an ADH22 polymorphism, while whites have ADH21. ADH2*2 has a much higher Vmax, causing toxic buildup of acetaldehyde very quickly.

Additionally, half of asians have an Aldehyde dehydrogenase which makes a slower conversion to acetic acid, making them even less able to detoxify the acetaldehyde which is being quickly produced.

Question 28

What is the nomenclature for ADH?

Answer 28

Humans have 7 ADH enzymes grouped into 5 classes.

1, 2, and 3 encodes alpha, beta, and gamma polypeptides respectively.

In the asian vs white example, we were focusing on ADH2 (beta peptides)